Potential energy is the energy of a particle that it possesses because of it's position relative to other particles. Usually we think of a particle and it's relationship to a field, where the field has been generated by another particle. e.g. gravitational field and mass.
E=mc^2 is a truncated term that comes from the Relativistic Energy-mass equivalence. (As Hitmouse stated!) It comes about because the conservation of mass didn't work in special relativity and therefore it was required to 'fold in' the conservation of Energy also to make it work. Thus one finds that the universe can convert mass to energy and energy to mass.
The full term is
Now if we take the frame of reference of any individual particle, called the centre of mass frame I think, it is stationary therefore it has zero velocity and p=0 and the familiar E = m_0 c ^2 drops out. However if we look at the particle from another frame of reference - say a moving frame - then we also need, in order to be exact, to add the momentum term.
At no point have I talked about any other particle or field to derive this equation thus it is not a potential energy. Or at least potential energy as defined by physics.
I see where you are coming from, I think....but because energy and mass are equivalent and these are conserved, in a closed system the value of 'E' is a constant. On the other hand, a particle in a field can vary the total energy of the system by moving in the field, and this is what we mean by potential energy.